In 1996, Clarke won his second European Tour title at the Linde German Masters by one stroke, shooting a final round 63 to finish 24 under par, one stroke ahead of Englishman Mike Davis. Clarke also recorded his best finish in a major, at that current time, with a tie for 11th place at The Open Championship in 1996. He also equalled his best finish on the Order of Merit, placing in 8th for the season.
He met his wife Heather in a nightclub in Portrush, County Antrim, and they married in March 1996. The couple had two sons, Tyrone and Conor, and the family lived at Sunningdale, Berkshire, UK. In 2005 and 2006 he missed several tournaments to care for his wife, who had been diagnosed with both primary breast cancer in December 2001, then, in 2004, with secondary breast cancer. Heather Clarke died on Sunday 13 August 2006 at 39 years of age, in the Royal Marsden Hospital, London.